The steinbock framework can be used programmatically using the steinbock Python package.
In this section, the installation of the steinbock Python package is described.
For scripting use only
Installing/using the steinbock Python package directly is not recommended for regular users. Please use the steinbock Docker containers instead.
Python 3.8 or newer
Tested versions of Python package dependencies can be found in requirements.txt.
The steinbock Python package can be installed from PyPI as follows:
pip install steinbock
The following extras are available:
imcto enable IMC preprocessing functionality
deepcellto enable DeepCell segmentation functionality
To install all extras, use the
pip install "steinbock[all]"
Package version conflics
Some of the dependencies of steinbock are incompatible due to different version requirements. As a workaround, use the following strategy for installing tested combinations of package versions:
# choose between one of the following: # pip install --upgrade -r requirements_deepcell.txt # pip install --upgrade -r requirements_deepcell-gpu.txt pip install --no-deps deepcell==0.12.2 pip install --upgrade -r requirements.txt pip install --no-deps "steinbock[all]"
Please refer to Python usage for usage instructions.